Hello Neelaish,
do you have access to this example? https://www.mathworks.com/help/autoblks/ug/generate-parameter-data-for-estimations-circuit-battery-block.html
It's for a higher order RC pair, but aligns specifically with what you are doing.
Here is some extra documentation for it: https://www.mathworks.com/content/dam/mathworks/tag-team/Objects/s/76117-sae-2013-battery-estimation-layered-technique.pdf
If these aren't helpful, are you able to share your model, or could you contact technical support and share it with them if it is not appropriate to be posted publicly?
Regards,
Joel